Contacts of the helix formed by residues 753 - 763 (chain A) in PDB entry 2XER
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ARG 753 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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748A SER* 4.8 9.5 + - - -
751A VAL 5.6 0.7 - - - -
752A ASP* 1.3 77.4 - - + +
754A GLN* 1.3 71.8 + - - +
756A LEU* 3.6 26.8 - - - +
757A ASN* 3.2 29.4 + - - +
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Residues in contact with GLN 754 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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752A ASP* 3.2 21.3 - - + +
753A ARG* 1.3 86.0 - - - +
755A LYS* 1.3 65.2 + - + +
757A ASN* 3.5 11.3 + - - +
758A LEU* 3.5 17.3 + - - +
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Residues in contact with LYS 755 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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726A LEU* 3.5 30.6 - - + +
751A VAL* 3.1 23.8 - - + -
752A ASP* 3.2 21.3 + - - +
754A GLN* 1.3 76.9 - - + +
756A LEU* 1.3 64.4 - - - +
758A LEU* 3.0 31.6 + - + +
759A LEU* 3.2 12.3 + - - +
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Residues in contact with LEU 756 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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744A VAL* 3.9 24.5 - - + +
747A PHE* 3.7 33.9 - - + +
748A SER* 3.1 31.0 - - - +
751A VAL* 3.7 8.0 - - + +
752A ASP 2.9 19.1 + - - +
753A ARG* 3.6 27.4 - - - +
754A GLN 3.3 0.2 - - - -
755A LYS* 1.3 77.7 - - - +
757A ASN* 1.3 64.2 + - - +
759A LEU* 3.2 9.6 + - + +
760A GLU* 3.1 24.8 + - + +
765A LEU* 5.4 1.8 - - + -
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Residues in contact with ASN 757 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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753A ARG* 3.2 14.2 + - - +
754A GLN* 3.7 10.5 - - - +
756A LEU* 1.3 78.1 - - - +
758A LEU* 1.3 67.9 + - + +
760A GLU* 3.3 22.7 + - - +
761A THR* 3.1 27.8 + - - +
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Residues in contact with LEU 758 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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726A LEU* 5.1 10.8 - - + -
754A GLN 3.5 14.8 - - - +
755A LYS* 3.0 29.5 + - + +
757A ASN* 1.3 79.9 - - + +
759A LEU* 1.3 56.8 + - + +
761A THR* 3.7 4.3 + - - -
762A LYS* 2.8 37.1 + - + +
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Residues in contact with LEU 759 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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722A THR* 5.0 5.6 - - + -
725A LEU* 3.9 23.1 - - + -
726A LEU* 3.4 34.8 - - + -
747A PHE* 3.7 40.6 - - + -
751A VAL* 5.1 5.4 - - + -
755A LYS 3.2 7.9 + - - +
756A LEU* 3.2 11.9 + - + +
758A LEU* 1.3 78.0 - - - +
760A GLU* 1.3 66.4 + - - +
762A LYS* 3.4 14.8 - - + +
763A LEU* 2.9 36.9 + - + +
765A LEU* 4.2 13.6 - - + +
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Residues in contact with GLU 760 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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744A VAL* 4.2 25.7 - - + +
756A LEU* 3.1 16.6 + - + +
757A ASN* 3.3 29.2 + - - +
759A LEU* 1.3 76.6 - - - +
761A THR* 1.3 60.0 + - - +
764A GLN* 2.9 30.3 + - - -
765A LEU* 3.1 32.9 + - + +
766A VAL* 6.1 0.2 - - - -
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Residues in contact with THR 761 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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730A GLN* 3.8 10.9 + - - -
757A ASN* 3.1 14.5 + - - +
758A LEU* 4.2 4.3 - - - -
760A GLU* 1.3 77.6 - - - +
762A LYS* 1.3 61.0 + - - +
764A GLN* 4.2 16.5 + - - +
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Residues in contact with LYS 762 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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725A LEU* 3.4 22.1 + - + +
726A LEU* 4.1 11.4 - - - +
728A ILE* 2.6 34.9 + - - +
729A PRO* 3.7 1.2 + - - +
730A GLN* 3.0 54.5 + - - +
733A LEU* 3.9 13.2 - - + +
758A LEU* 2.8 25.0 + - + +
759A LEU* 3.4 19.1 - - + +
760A GLU 3.0 0.6 - - - -
761A THR* 1.3 80.2 - - - +
763A LEU* 1.3 67.1 + - + +
764A GLN* 3.7 0.4 - - - -
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Residues in contact with LEU 763 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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686A LEU* 4.9 15.5 - - + -
690A LEU* 4.7 16.6 - - + -
725A LEU* 4.5 24.9 - - + -
733A LEU* 3.4 32.3 - - + -
736A PRO* 5.1 14.0 - - + +
739A ILE* 4.0 15.6 - - + +
747A PHE* 4.7 5.6 - - + -
759A LEU* 2.9 25.1 + - + +
762A LYS* 1.3 81.7 - - + +
764A GLN* 1.3 71.6 + - - +
765A LEU* 2.9 29.2 + - + -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il